Can HaplotypeCaller be used on drug treated samples?
Hello, I am working on a RNASeq data which consists of liver samples from donors. It is a case-control study where 12 samples are divided as Normal (control) and Rifampin Treated (case). I want to...
View ArticleGATK ERROR MESSAGE: 38 HaplotipeCaller
Hello everyone, I´m using HaplotypeCaller program in whole sheep genome. The next paragraph is the command used for all 158 samples. We use nodes of 16 cores (-ntc 16) and 28 Gb of memory RAM. Could...
View ArticleProblems with BAMs decompressed from CRAMs
I have a number of NGS samples, with 30x coverage. Samples were processed according to GATK Best Practices. For some samples, the processed BAMs were kept, for others BAMs were compressed to CRAMs. My...
View ArticleTraining GATK4
Hi, I'm a researcher in Italy and I'm looking for a research center in Europe that I can be a host for a short training on GATK4. I'm new in GATK and I'm building the pipeline on Bash. For now I don't...
View ArticleMutect2 version 4.0.0.0
Mutect2 version 4.beta.6 ./gatk-launch Mutect2 --help BETA FEATURE - FOR EVALUATION ONLY Mutect2 version 4.0.0.0 ./gatk Mutect2 --help BETA FEATURE - WORK IN PROGRESS Is there a timeline for having a...
View ArticleWeb-based Oncotator server
There is a web-based version of Oncotator which you can use for annotation without running anything on your own machine. However, please note that the web-based version is an older version, with fewer...
View ArticleClik here to view.
Can I use GATK on non-diploid organisms?
In general most GATK tools don't care about ploidy. The major exception is, of course, at the variant calling step: the variant callers need to know what ploidy is assumed for a given sample in order...
View ArticleTrouble with running GenomicsDBImport
I'm writing a pipeline using GATK4 for our local cluster which uses Slurm as job scheduler. The command below seems to run successfully, however, it took only a few seconds and the output file sizes...
View ArticleBQSR and Novaseq quality scores
Dear all, we recently bought an Illumina Novaseq instrument and as a first project sequenced some human whole genomes. Since the Novaseq only has 4 quality scores (2, 11, 25 and 37) I was wondering if...
View ArticleGermline copy number variant discovery (CNVs)
Purpose Identify germline copy number variants. Diagram is not available Reference implementation is not available This workflow is in development; detailed documentation will be made available when...
View ArticleGATK4 results for PrecisionFDA Consistency challenge data
Dear team, I've run GATK4.0.0 using Cromwell (30.2) and WDLs at https://github.com/gatk-workflows/gatk4-data-processing and https://github.com/gatk-workflows/gatk4-germline-snps-indels. I had bwa...
View ArticleWhat is correct way to generate the input vcf and vcf.idx file for GATK4
Hi, We want to call SNVs by M2 for our WGS data. But, we do not have gnomad.vcf for WGS. So, we downloaded vcf files for each chr from gnomad website. Could you please let me know the "correct" way to...
View ArticleVariantRecalibrator Stack Error
Hi, I tried to run VariantRecalibrator for one WGS sample after HaplotyopeCaller. But I got stack trace error. The commands I run is below. java -Xmx4g -Djava.io.tmpdir=tmp -jar...
View Article[ERROR] SelectVariants
Hi, I want to run SelectVariants on FC using my own vcf. But, I got the following ERROR. Any suggestions are welcome. Thanks! Best, Chunyang 22:08:56.550 INFO SelectVariants - Initializing engine...
View ArticleHow can I exclude multi-mapped reads before using UnifiedGenotyper to call SNPs
Hi, how can I exclude multi-mapped reads before using UnifiedGenotyper to call SNPs? You mentioned picard that could be used to exclude multi-mapped reads. However, which tool of picard should be used?...
View ArticleHaplotypeCaller and reads mapped to multiple locations
Dear GATK team, I've been trying to use GATK to call SNPs from RNA-Seq data mapped to a transcriptome assembly. I used Bowtie2 for the read mapping. I apologize if the information is already posted,...
View ArticleElapsed time about the CNVDiscoveryPipeline
@bhandsaker Hi Bob,why does the CNVDiscoveryPipeline is so time consuming? I test a WGS sample (about 30x),and run about 4 days,and it is still runing.This is my script about the CNVDiscoveryPipeline:...
View ArticleClik here to view.
MuTect2 Seems to lose a lot of mutations.
I use Mutect2 (tumor only mode) to find somatic mutation, but some position was not able find mutations. I have attached some IGV figures in the regions where MuTect2 has missed somatic mutations (Top...
View ArticleCalculateMixingFractions Returns all NaN?
Hi there, I'm attempting to use the CalculateMixingFractions tool to estimate the mixture of genomes from a VCF in a pooled BAM file and getting all NaN as output. The output looks like this: SAMPLE...
View Article(howto) Recalibrate base quality scores = run BQSR
Objective Recalibrate base quality scores in order to correct sequencing errors and other experimental artifacts. Prerequisites TBD Steps Analyze patterns of covariation in the sequence dataset Do a...
View Article